Thanks Joao Henriques for helping me with the steps. On Nov 4, 2013 3:18 PM, "João Henriques" <joao.henriques.32...@gmail.com> wrote:
> Hello Archana, > > I'm also toying with a TFE-water system, therefore I am also a newbie. This > is what I am doing, I hope it helps: > > 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I > don't use PRODGR, see why in DOI: 10.1021/ci100335w). > 2) Do the math and check how many molecules of TFE you're going to need for > a given v/v TFE-water ratio and a given simulation box volume. > 3) Build box with the correct size. > 4) Randomly insert correct number of TFE molecules. > 5) Solvate. > 6) Insert protein. > > Hopefully, the amount of TFE and water molecules that will be deleted in > inserting the protein in the final step will be proportional, given that > the TFE molecules are well distributed. > > I've tried many different ways of doing this and it's always impossible to > maintain a perfect TFE-water ratio, no matter the order and manner of > insertion of each system component. I've also never been able to insert the > correct number of waters after the TFE. My calculations predict a higher > number, but the solvation algorithm can't find enough space for them. > > In sum, either you place each molecule by hand and you spend a life time > building the system, or you just make a few compromises and deal with it. I > ended up going with the former as I have a limited amount of time on my > hands and I am aware of the approximations I am doing. > > Best regards, > > João Henriques > ------------------------------------------------ > PhD student > Division of Theoretical Chemistry > Lund University > Lund, Sweden > ------------------------------------------------ > joao.henriq...@teokem.lu.se > http://www.teokem.lu.se/~joaoh/ > > > On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: > > > >> Dear Justin, > >> > >> I have not constructed the system but I have downloaded it from ATB > >> website. To maintain the number of TFE and water molecules(1:1 v/v) in > the > >> system (I don't want to add extra water molecules) I tried many options > in > >> genbox but still it adds 678 water molecules. Can you provide me some > >> hint? > >> > >> > > Not without seeing your actual command(s). > > > > > > Is their need to remove periodicity of this pre-equilibrated system as > in > >> case of lipids? > >> > >> > > No idea. Are the molecules broken in the initial configuration? > > > > -Justin > > > > -- > > ================================================== > > > > > > Justin A. Lemkul, Ph.D. > > Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 601 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > > ================================================== > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists